Silver Salt Analysis


This document describes how to set up and run nitrate or sulfate for Δ17O on the Lorax, ThermoFinnigan MAT 253. Silver nitrate samples (loaded into silver capsules) or silver sulfate samples (loaded into quartz or gold capsules) are dropped by an autosampler into a hot quartz pyrolysis reactor within a Temperature Conversion Elemental Analyzer (TCEA). A helium carrier stream moves pyrolysis products through a liquid nitrogen trap where byproducts other than O2 are frozen. The O2 product then continues through a gas chromatograph and either a Conflo or Gasbench interface. The Conflo is used for samples of O2 &grt; 2 μmol; the Gasbench cryofocuses O2, enabling analysis of smaller samples (50-1000 nmol). Make sure the sample is <1000nmol when using Gasbench mode. Helium continues to move O2 into the mass spectrometer for m/z 32, 33, and 34 measurements.

For clarity, sections specific to the Conflo mode will have a Conflo tag while the Gasbench mode will have a Gasbench tag.

This general plumbing diagram and this gasbench valco valve diagram may help your understanding of the system.


Appropriate precautions should be taken to protect yourself against extreme temperatures as you will encounter a range from very cold liquid nitrogen temperatures to very hot baking-out parts. Wear eye protection and leather gloves when handling these extreme temperature items.


Nomenclature - All of the terms, acronyms, and colloquialisms that apply to this SOP can be found in the nomenclature section below.

Conflo vs Gasbench - Samples can be analyzed across a reasonably wide range of sulfate or nitrate amounts. The larger samples (e.g. 1-10 µmol) are measured using Conflo mode while smaller samples (e.g. <1 µmol) are measured using Gasbench mode. Switching between these two modes requires careful attention to detail and patience.

Pyrolysis column - The pyrolysis column is the temperature-controlled location of the reaction inside the TCEA. Silver nitrate samples use a reaction temperature of 585 °C and silver sulfate samples use a reaction temperature of 1000 °C. The pyrolysis column needs to be cleaned out after each run of samples.

Sample Loading - Most of the work associated with loading samples into the instrument is spent purging atmospheric air out of the autosampler. Take your time in this section to minimize backgrounds and the size of the O2 blank.

Run sequence - You will create a run sequence in the Isodat software that will include sample identifiers, amount of material, run method, and other details pertaining to each individual sample capsule.

Daily Log - We use daily logs for all our instrumentation to keep us organized, account for usage, and make certain the instrument is ready for our samples.

Start your run - If you have made it this far, the instrument must be ready and it is time to start your run.

Instrument bake-out - Consider baking out the instrument after each run. This may not be required but baking the entire set-up is at least an overnight time commitment.

Troubleshooting - If something does not seem right, check here.

Suggested Reading - There are always more papers to read.



Liquid nitrogen traps

TCEA liquid nitrogen traps for cleaning the helium before entry into the pyrolysis reactor and after pyrolysis to trap the unwanted byproductsClick to enlarge.
TCEA liquid nitrogen traps.
Gasbench liquid nitrogen traps for concentrating and cryofocusing sample oxygenClick to enlarge.
Gasbench liquid nitrogen traps


The three TCEA autosampler valves used when preparing the autosampler to run your samplesClick to enlarge.
TCEA autosampler valves
Three TCEA helium flow manipulation valves for diverting flow or changing analysis modesClick to enlarge.
TCEA helium valves
Two lorax needle valves for changing among Gasbench, Conflo, and dual-inlet methodsClick to enlarge.
Lorax needle valves

Conflo vs Gasbench

Samples can be analyzed across a reasonably wide range of sulfate or nitrate amounts. The larger samples (e.g. 1-10 µmol) are measured using Conflo mode while smaller samples (e.g. <1 µmol) are measured using the Gasbench mode. The Gasbench is further separated into two modes: "Split-out" and "Split-in". Split-out is for 300 to 1100 nmol samples while Split-in should be used for tiny samples (e.g. <300 nmol). These two modes are named after the peripheral that precedes the inlet to the mass spectrometer.

Adjusting the needle valves

If you are switching from one mode to another, you will need to close one needle valve and open the other. You may also be switching from dual-inlet mode to conflo or gasbench, in which case you will need to open the appropriate needle valve. Use the photo above to identify the specific needle valve of interest.

  1. To close a needle valve, make sure the vacuum is visible from within the Isodat software (you can hover the mouse over the high vacuum reading and it will magnify) while you stand at the needle valves. Close the valve ONLY as much as needed. YOU CAN CLOSE IT TOO MUCH AND RUIN THE VALVE. Watch the vacuum reading and begin twisting the needle valve closed (clockwise, righty tighty). When vacuum decreases to <3e-8 mbar, stop twisting. WAIT. If vacuum doesn’t appear to be decreasing any more, GENTLY close the needle valve some more. If the vacuum responds, WAIT and repeat.
  2. The appropriate needle valve should be open the day before you intend to run to allow the fused silica capillary time to purge with helium.
  3. Conflo - Make certain the dilution is ON (within the left side of the Isodat software under the Conflo panel) before attempting to open the needle valve.
  4. Just as with closing a needle valve described above, make the vacuum visible while you are standing at the needle valves.
  5. VERY SLOOOOOWWWWLY open the appropriate needle valve watching the vacuum. You will see the vacuum rise from <2e-8 mbar to ~1e-6 mbar (it may be in the 9e-7 range). If the vacuum reading jumps into the Xe-5 range and stays there, close the needle valve. Verify that helium is in fact flowing to the peripheral of interest and try again. If it still remains in the Xe-5 range, close the needle valve and seek advice.
  6. If you have just opened a needle valve that was previously closed, run an 8 hour bake-out sequence for the appropriate mode (Conflo vs Gasbench).


In the lower left corner of Isodat, use the menu to select Conflo or GasBench.

Pyrolysis Column

The pyrolysis column is an empty quartz reactor with a restriction at the base of the TCEA hot zone (the vertical space along which the temperature is held at your set point) to catch sample capsules and allow the reaction to take place at the set temperature. The sample capsules must be cleaned out after each run. The reactor can accommodate many more nitrate samples than sulfate samples because the nitrate samples are wrapped up tightly into a small silver capsule while sulfate samples are loaded into more bulky quartz or gold capsules. About 10 quartz capsules will fit into the reactor before they start piling up high enough to leave the hot zone. Silver metal and other condensables adhere to the side walls outside of the hot zone and eventually may affect your analysis (see anti-blank below) making it best to start with a new reactor.

As of today (2022-09-27), the column design has a pinch point at 32 cm from the top of the column. We are using quartz tubes from EA suppliers that have a 2 mm wall thickness. The pinch is created on a vacuum line in the wet lab and the "quartz" torch tip. The hot-zone based on the discoloration of the column after many sulfate samples (and as of 2022-09-27) is between 22 cm and 32.5 cm.

  1. You will either need to clean out the previous runs capsules or replace the pyrolysis tube before starting a new run.
  2. Conflo - Turn the He dilution ON if running Conflo mode.
  3. Gasbench - Change the Valco Valve to Inject if running in Gas Bench mode.
  4. Turn the Vent Valve to vent.
  5. Turn the Autosampler 3-way valve to vent.
  6. Use gloves and protective eye-wear. Unscrew the pyrolysis column starting at the top by loosening the nut all the way, removing the autosampler, and setting the autosampler on top of and towards the back of the TCEA.
  7. Unscrew the bottom fitting and remove the body, nut and two teflon ferrule pieces.
  8. Remove pyrolysis tube by pushing the bottom up and grabbing the metal bushing and o-ring and place in the pyrex baking dish.
  9. Select a new pyrolysis tube or clean out the existing one with the wire-tipped wand.
  10. Place the metal bushing and rubber o-ring on top of the new pyrolysis column about 5 mm from the top. Use compressed air (red tube above TCEA) to clean any dust off the teflon ferrule. Slide pyrolysis tube into TCEA. Start at the top of the TCEA. While bearing the weight of the autosampler, screw on the top column nut and use a spanner to tighten an additional quarter turn. Now move to the bottom of the column. Use compressed air to cool the bottom of the tube that just went through the furnace. Slide fitting onto the pyrolysis tube as high as it can go and ensure you have the proper order of the nut, back of ferrule, and front of ferrule and then finger tighten. Use wrenches to tighten an additional quarter to half turn. DO NOT OVERTIGHTEN.
  11. The top rubber ferrule will compress over time, but will recover if allowed to rest for a few days – swap it with another rubber ferrule when it looks compressed or is leaking. The bottom Teflon ferrules compress over multiple uses. Once they start leaking (or get dirty), they must be replaced with new ferrules.
  12. Close the 3-way valve.
  13. Use the leak detector to check for leaks. Check around both top and bottom fittings. If leaks are present, consider tightening fittings or repeat process of loading the pyrolysis tube without actually removing the column.
  14. Once leaks are eliminated, leave Vent Valve in vent position for ~10 minutes before switching to run.

Sample Loading and Autosampler Purging

Each sulfate run may contain a maximum of 10 samples in quartz or gold capsules. Nitrate runs may contain up to a full carousel (49 balled silver capsules). The goal in this section is the load your samples and then ensure all of the atmospheric air that was allowed into the autosampler is purged out and replaced with helium.

  1. Isolate the autosampler by closing the Isolation Valve. Rotate the valve 90°; the arrow on side of valve will be pointing towards you and you won’t be able to see down inside the reactor.
  2. Turn the Autosampler 3-way Valve clockwise to vent pressure from inside the autosampler. The valve handle will point towards the Lorax computer.
  3. Loosen the three knurled nuts that clamp the autosampler lid into place (you may need a spanner). Open the lid and use compressed air to clean out any debris.
  4. Load samples into slots. Close the lid, and gradually hand tighten each clamp a little at a time, alternating between nuts to ensure even pressure.
  5. Turn Autosampler 3-way Valve 180° counter-clockwise to evacuate the autosampler. While it’s evacuating, tighten the nuts onto the lid with your fingers again.
  6. After 3-5 minutes, turn Autosampler 3-way Valve to point straight back (off position).
  7. Slowly open He Purge Valve. Monitor pressure on the front of TCEA until it levels off (Purge=1.5 bars and Carrier=1.5 bars).
  8. Use leak detector to check for autosampler leaks around the lid as was done for the reactor.
  9. If no leaks are found, slowly turn the Autosampler 3-way Valve clockwise until the helium vents and the pressure gauges drop. Then turn the Autosampler 3-way Valve counter clockwise to the closed (straight back) position. Once the pressure gauges read 1.5 bars, vent the helium again and repeat 10-12 times.
  10. Conflo - Ensure the dilution is ON.
  11. Gasbench - ensure the Valco Valve is in the Inject position.
  12. Open the Isolation Valve (rotate it until the arrow is pointing up).
  13. Conflo - Monitor the O2 background and keep venting helium from the autosampler as in the above step until the backgrounds are sufficiently low.
  14. Gasbench - We can't use real-time backgrounds because the TCEA is never in a direct flow path with the mass spectrometer and we must use a different technique outlined below. For now, we will blindly do our best.
  15. Conflo - Monitor the O2 background signal for ~5 minutes. If the background has not increased dramatically since opening the Isolation Valve, turn the dilution off.
  16. Place the clean-up traps in the dewar and fill the dewar with liquid nitrogen.
  17. Close the purge valve.
  18. Vent the helium using the Autosampler 3-way Valve as above but this time the pressure gauges will NOT drop (because the purge valve is closed). Wait about one minute. Repeat this venting 5-10 times.
  19. Conflo - Monitor the O2 background signal for ~ 5 minutes. If it is not rising proceed to the next section, otherwise repeat the above venting procedure and or check for leaks.
  20. Gasbench - Proceed to the next section but realize you may purge more after you see the size of your blanks.

Run Sequence

Create a sequence using the IsoDat Acquisition software (if Acquisition is already running something you can use Workspace instead). All of the data you type into the sequence are exported with the data. Isodat saves the sequence file upon starting a run. Saving a unique version of the sequence itself is not required.

  1. Conflo - Generally use the Conflo_O2_Samples.seq sequence.
  2. Gasbench - Generally, use the GasBench_O2_Samples.seq.
  3. Make sure a check is in every box in the "Peak Center" column.
  4. Record the amount of expected O2 for each sample (μmol or nmol) under "Amount".
  5. Enter sample name or ID under "Identifier 1" and any other information under "Identifier 2", "Comment", and "Preparation"
  6. Make sure the appropriate method (*.met) is selected under the "Method" header.
    • Conflo - We usually have a “Zero” at the beginning and end of the run, as well as in between each sample. Make sure that Zero runs use method Conflo_O2_Zero.met and sample runs use method Conflo_O2_Sample.met.
    • Gasbench - Include at least three “Blanks” at the beginning and end of the run, as well as at least one in between each sample. Make sure the blanks use method GasBench_O2_Blk_*.met and samples use GasBench_O2_Sample_*.met, where * is either "SplitIN" or "SplitOUT". We suggest using "SplitOUT" for samples amount between 300 and 1100 nmol.
  7. Save the sequence. Again, saving a unique version of the sequence itself is not required because everything you enter into a sequence is written to the exported data file.

Daily Log

The lab uses a daily log for each instrument or preparation line to allow users a first glance at the readiness of the instrument. By comparing the current state of the instrument to historical states, you are more informed about the instrument and whether or not it is functioning properly and ready to run your samples.

Each daily log is web based and browser accessible. No link is provided here by design. Open the browser on the controlling computer and you should see at least two tabs already open. One tab is this SOP and the other is the daily log. If the browser has more than two tabs open, it may have additional SOPs. Use the bookmark toolbar as needed if tabs have been closed.

Work through each cell of the daily log. If you are uncertain where to find certain information, hover over the column header tip, denoted by a ⓘ symbol.

Make certain to press the 'save to log' button when you are finished entering data.

You are welcome to make notes if you have observed something with or done something to the instrument and would like to document that information. Use the "insert note" link at the top of the daily log to make a note. You may enter notes at any time.

Start Your Run

Check List

Well done. You made it this far. We will go through a quick check list and then start.

Start the run

Now What?

Post-run cleanup and instrument bake-out

For maximum efficiency, these steps happen immediately after a run has finished. It is also good practice to complete the bake-out routine before (not necessarily immediately before) starting another set of samples. If you are still in the lab after a run finishes and have about 30 minutes, complete these steps. Otherwise, try to complete them the following day or at least prior to a future run.

Liquid nitrogen and pyrolysis column

  1. When a run is done (in either Conflo or Gasbench mode), turn the vent valve to “Vent” mode and thaw the TCEA cleanup trap by removing it from the liquid nitrogen dewar and heating it on ‘HI’ for 5 minutes. This is designed to remove most of the trapped SO2 that may be present and allow it to go out the vent through the snorkel hood in the ceiling.
  2. Pour any leftover liquid nitrogen back into a storage dewar.
  3. Clean out the pyrolysis column as described above under Pyrolysis Column.
  4. Change the Vent Valve back to run mode.
  5. When running is Gas Bench mode, make sure the Valco valve is in “Inject” mode (toggle on the IsoDat control screen). Pour any leftover liquid nitrogen from the large blue dewar back into a storage dewar.

8-hour Gasbench Bake Routine - Use this bake sequence when actively running in Gasbench mode or if you have just switched to Gasbench mode and want to give the system and initial bake.

8-hour Conflo Bake Routine - Use this bake sequence when actively running in Conflo mode or if you have just switched to Conflo mode and want to give the system and initial bake.

Ending the Bake Routine

Data processing

While the data processing is entirely up to you, I suggest running the python script loraxGB.py and then loraxGBcalibrate.py. The goal here is the monitor instrument performance and be able to easily compare new runs with historical runs.

  1. Copy the .csv file from the Lorax computer to the data server (S:). The python scripts are setup to use S:\Data\lorax\gasbench\raw\.
  2. On one of the Zax computers, open a cmd prompt, type 'S:', then enter, then 'cd Data\python\', then enter.
  3. Type 'py loraxGB.py' and hit enter. This takes your recent run(s) and puts all the data into S:\Data\projects\lorax\gasbench\loraxGB_analysis_log.csv, which is a log file of all analyses for the current session.
  4. Type 'py loraxGBcalibrate.py'. This reads in the log file mentioned above and creates figures saved to an .html page.
  5. In S:\Data\projects\lorax\gasbench\figs\, double click on 'open-me-to-view-figures.html' and the latest figures will be viewable in the defualt browser.
  6. That is it for now. Certainly more needs to be done here...


Suggested Reading


I have read and understood the present SOP and, before starting work outlined in the present SOP, I will complete all required training.

Last updated: 2022-09-27 10:29:32